RetrogeneDB ID: retro_ggor_1990

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:160505966..160506434(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: C9ORF78
• Ensembl ID: ENSGGOG00000013358
• Aliases: None
• Description: None

Sequence

>retro_ggor_1990
AAGATAAAATCAGTGAAGAGGAAGACCCTGGGGACATTGTTTTCTGCAGAAACCAACTGAAGGGATGAGAATGCAGACAT
AATAAAGTACGTTGAGACAGAGCTGAAGAAGAGGAAAGAGACTATGGAACATAAGGAACAGAAAGTAAAGCTGAAGAACA
CAGAGGACTGCCTTTATGAACTTCAAGAAAACATTTGTGTTTCCTCAGCAAAGAAGACAGAGGAGATGCTTTCTAGCCAG
ATGCTGAGTGGCATCCCCAAGGTGGACCTCAGCATCAATGCTAAAATAAAAAAATAATATCATTTCCATGGAGGATGCCA
AAGCCCAGCTGGGGAAGAACAGCAGAACAAGAAGAAAGACAGTGAGACGTCCTTCGTGCCTACCAACGTGGCTGTGAATA
TATGCTGCACAGCCGATTTTTATCATTAGGAGCTCAACAGCCTCATACACAGAAACAAAGAAGAGCCT

Alignment

ORF - retro_ggor_1990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 53.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVKPKNAEDCLYELPENIRVSSA
          KI.......LGT.FSAETN.RDE.AD..KY.ETELKKRK...EH.EQKVK.KN.EDCLYEL.ENI.VSSA
Retrocopy KIKSVKRKTLGTLFSAETN*RDENADIIKYVETELKKRKETMEHKEQKVKLKNTEDCLYELQENICVSSA

Parental  KKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQ-NKKKDSETSFVPTNMAVN-YVQHNR
          KKTEEMLS.QMLSGIP.VDL.I.AKIK..............E.Q.NKKKDSETSFVPTN.AVN.Y..H.R
Retrocopy KKTEEMLSSQMLSGIPKVDLSINAKIKK*YHFHGGCQSPAGEEQQNKKKDSETSFVPTNVAVN<YMLHSR

Parental  -FYHEELNAPIRRNKEEP
          .FYH.ELN..I.RNKEEP
Retrocopy >FYH*ELNSLIHRNKEEP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.05 RPM	68.81 RPM
SRP007412_cerebellum	0.00 RPM	57.13 RPM
SRP007412_heart	0.03 RPM	19.61 RPM
SRP007412_kidney	0.04 RPM	78.26 RPM
SRP007412_liver	0.00 RPM	33.18 RPM
SRP007412_testis	0.00 RPM	71.48 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1990 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2872
Pan troglodytes	retro_ptro_1943
Macaca mulatta	retro_mmul_1460

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990 ,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,